Franck Lejzerowicz

• Calderón-Osorno, Melany; Barrantes-Jiménez, Kenia; Lejzerowicz, Franck Laurent Patrick; Arias-Andres, Maria & Rojas-Jimenez, Keilor (2026). Insights into the riverine metaplasmidome: The role of anthropogenic factors in shaping microbial communities. The Microbe. 10, p. 1–11. doi: 10.1016/j.microb.2025.100640. Full text in Research Archive Show summary

  The environmental plasmidome, encompassing the collective plasmids within an ecosystem, plays a key role in microbial adaptation and evolution. Plasmids, as mobile DNA molecules, enable the transfer of beneficial traits among bacteria, especially in response to environmental stresses. In this study, we developed a novel protocol combining PlasmidSafe DNase and REPLI-g amplification to selectively enrich and characterize plasmidic DNA from polluted environments. We applied this approach to the Virilla River (Costa Rica), a system heavily impacted by urban and industrial activities, analyzing water and sediment samples across seasons and pollution gradients. Our method enabled the recovery of longer, circular contigs confidently identified as plasmids through multiple independent tools, with 28,043 circular sequences primarily linked to Gammaproteobacteria. Contaminated sites, particularly during the rainy season, showed higher plasmid diversity and a marked increase in antibiotic resistance genes (ARGs). This heightened diversity in contaminated environments has implications for the dissemination of antibiotic and metal-resistance genes, as well as other adaptive traits within microbial communities. This research underscores the need to study plasmids in natural environments to better comprehend their ecological roles and potential risks in polluted ecosystems.

• Barrantes-Jiménez, Kenia; Lejzerowicz, Franck; Tran, Tam; Calderón-Osorno, Melany; Rivera-Montero, Luis & Rodríguez-Sánchez, César [Show all 11 contributors for this article] (2025). Anthropogenic imprint on riverine plasmidome diversity and proliferation of antibiotic resistance genes following pollution and urbanization. Water Research. ISSN 0043-1354. 281. doi: 10.1016/j.watres.2025.123553. Full text in Research Archive Show summary

  Plasmids are key determinants in microbial ecology and evolution, facilitating the dissemination of adaptive traits and antibiotic resistance genes (ARGs). Although the molecular mechanisms governing plasmid replication, maintenance, and transfer have been extensively studied, the specific impacts of urbanization-induced pollution on plasmid ecology, diversity, and associated ARGs in tropical regions remain underexplored. This study investigates these dynamics in a tropical aquatic ecosystem, providing novel insights into how pollution shapes plasmid composition and function. In contrast to the observed decrease in chromosomal diversity, we demonstrate that pollution associated with urbanization increases the diversity and taxonomic composition of plasmids within a bacterial community (plasmidome). We analyzed eighteen water and sediment metagenomes, capturing a gradient of pollution and ARG contamination along a tropical urban river. Plasmid and chromosomal diversity profiles were found to be anti-correlated. Plasmid species enrichment along the pollution gradient led to significant compositional differences in water samples, where differentially abundant species suggest plasmid maintenance within specific taxonomic classes. Additionally, the diversity and abundance of ARGs related to the plasmidome increased concomitantly with the intensity of fecal and chemical pollution. These findings highlight the critical need for targeted plasmidome studies to better understand plasmids' environmental spread, as their dynamics are independent of chromosomal patterns. This research is crucial for understanding the consequences of bacterial evolution, particularly in the context of environmental and public health.

• Calderón-Osorno, Melany; Rojas-Villalta, Dorian; Lejzerowicz, Franck Laurent Patrick; Cortés, Jorge; Arias-Andres, Maria & Rojas-Jimenez, Keilor (2025). The influence of depth on the global deep-sea plasmidome. Scientific Reports. 15(1). doi: 10.1038/s41598-025-86098-5. Full text in Research Archive Show summary

  Plasmids play a crucial role in facilitating genetic exchange and enhancing the adaptability of microbial communities. Despite their importance, environmental plasmids remain understudied, particularly those in fragile and underexplored ecosystems such as the deep-sea. In this paper we implemented a bioinformatics pipeline to study the composition, diversity, and functional attributes of plasmid communities (plasmidome) in 81 deep-sea metagenomes from the Tara and Malaspina expeditions, sampled from the Pacific, Atlantic, and Indian Oceans at depths ranging from 270 to 4005 m. We observed an association between depth and plasmid traits, with the 270–1000 m range (mesopelagic samples) exhibiting the highest number of plasmids and the largest plasmid sizes. Plasmids of Alphaproteobacteria and Gammaproteobacteria were predominant across the oceans, particularly in this depth range, which also showed the highest species diversity and abundance of metabolic pathways, including aromatic compound degradation. Surprisingly, relatively few antibiotic resistance genes were found in the deep-sea ecosystem, with most being found in the mesopelagic layer. These included classes such as beta-lactamase, biocide resistance, and aminoglycosides. Our study also identified the MOBP and MOBQ relaxase families as prevalent across various taxonomic classes. This research underscores the importance of studying the plasmidome independently from the chromosomal context. Our limited understanding of the deep-sea’s microbial ecology, especially its plasmidome, necessitates caution in human activities like mining. Such activities could have unforeseen impacts on this largely unexplored ecosystem.

• Carlsen, Eira Catharine Lødrup; Wei, Jing; Lejzerowicz, Franck; Kjær, Sigrid Trier; Westermann, Sebastian & Hessen, Dag Olav [Show all 8 contributors for this article] (2025). Redox determines greenhouse gas production kinetics and metabolic traits in water-saturated thawing permafrost peat. ISME Communications. 5(1). doi: 10.1093/ismeco/ycaf009. Full text in Research Archive Show summary

  Redox conditions, influenced by the availability of oxygen, are expected to dictate the rate of CO2 and CH4 production and to shape the composition and metabolism of microbial communities. Here, we use thawing permafrost peat in thermokarst water under a gradient of initial O2 concentrations to experimentally cover the variability in redox conditions potentially found across thawing landscapes. The three main greenhouse gases, CO2, CH4 and N2O, responded differently to O2 absence. CO2 production along the O2 gradient could be modeled by the Michaelis Menten equation revealing a sharp decrease when oxygen dropped under 100 μM. Under anoxic conditions CO2 yield decreased by 98% and maximum net production rate by 85% when compared to oxic conditions during the 11 days after thaw. N2O production was observed under anoxic conditions, while CH4 yield and CH4 accumulation rates did not differ across the redox gradient. The latter is due to the release of stored CH4 due to thawing. Differences between oxic and anoxic conditions were reflected in the microbial genomic composition, with changes in taxonomic and functional groups, such as N2O reducers, fermenters, denitrifiers and sulfur reducers increasing under anoxic conditions. Genomic changes towards less efficient central metabolism further explained the CO2 production yields and rates limited by O2 availability as predicted by thermodynamics. Together with the Michaelis Menten models the metabolic reconstruction pinpoint to critical thresholds of CO2 release at suboxic conditions and thus need to be considered when explaining and modeling highly variable CO2 emissions across thawing landscapes.

• Tap, Julien; Lejzerowicz, Franck Laurent Patrick; Cotillard, Aurélie; Pichaud, Matthieu; McDonald, Daniel & Song, Se Jin [Show all 9 contributors for this article] (2023). Global branches and local states of the human gut microbiome define associations with environmental and intrinsic factors. Nature Communications. 14, p. 1–11. doi: 10.1038/s41467-023-38558-7. Full text in Research Archive

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• Schultze, Sabrina; Kamenova, Stefaniya Kamenova; Lejzerowicz, Franck Laurent Patrick; Gryn, Kristina; Hjerde, Erik & Åberg, espen [Show all 7 contributors for this article] (2026). Apple replant syndrome: An example for complex system dynamics affecting soil health. Full text in Research Archive Show summary

  In apple orchards trees are replanted every 15-20 years to increase yields. This is usually done in the same soil due to space restrictions. However that often leads to problems in growth and yield of the new trees. This problem is called replant syndrome.

• Schultze, Sabrina; Kamenova, Stefaniya Kamenova; Lejzerowicz, Franck Laurent Patrick; Gryn, Kristina; Hjerde, Erik & Åberg, espen [Show all 7 contributors for this article] (2026). Exploring microbial diversity in healthy and sick orchard soils: Insights into replant syndrome mechanisms. Full text in Research Archive Show summary

  Replant syndrome (RS), or sick soil syndrome, is a microbially mediated soil-borne syndrome that causes significant economic losses in orchards worldwide. It occurs where the same or closely related species are replanted, leading to reduced growth and yield quality. The mechanisms behind this syndrome remain poorly understood, suggesting a complex microbial dysbiosis. Our study examines the microbiomes of “RS-symptomatic” (hereafter: symptomatic soils) and “healthy” orchard soils in Norway. We hypothesized that healthy soils would harbour higher microbial biodiversity. We found that the average shoot length of the lowest seven branches of a tree was the best proxy for replant syndrome in our dataset, but geographic region had a stronger effect on growth patterns than soil health status. We found no significant correlation between chemical and physical soil variables and RS. Our findings based on DNA sequencing showed a higher eukaryotic (18S) Shannon alpha diversity in soil than in roots at all locations, while prokaryotic diversity (16S) was significantly higher in roots than in soil in only one region (Telemark). Comparing healthy and symptomatic soil, we found a significantly higher Shannon alpha diversity in healthy soil for 16S soil samples only in one region (Telemark), while there were no significant differences for 18S, and no significant differences in beta diversity for either. Again, region had a stronger effect on alpha biodiversity in 16S than soil health status, and was also significant in 18S. Average shoot length of the lowest seven branches was negatively correlated with 16S (soil) Shannon alpha diversity in RS soil only, a trend that was repeated but not significant for 18S in roots. We conclude that broad ecological perspectives are necessary to understand RS and highlight the need for studies focusing specifically on functional traits and the soil food web.

• Schultze, Sabrina; Kamenova, Stefaniya Kamenova; Lejzerowicz, Franck Laurent Patrick; Gryn, Kristina; Hjerde, Erik & Åberg, espen [Show all 7 contributors for this article] (2026). Exploring Microbial Diversity in Healthy and Sick Orchard Soils: Insights into Replant Syndrome Mechanisms. Full text in Research Archive Show summary

  Replant syndrome (RS), or sick soil syndrome, is a microbially mediated soil-borne syndrome that causes significant economic losses in orchards worldwide. It occurs where the same or closely related species are replanted, leading to reduced growth and yield quality. The mechanisms behind this syndrome remain poorly understood, suggesting a complex microbial dysbiosis. Our study examines the microbiomes of “RS-symptomatic” (hereafter: symptomatic soils) and “healthy” orchard soils in Norway. We hypothesized that healthy soils would harbour higher microbial biodiversity. We found that the average shoot length of the lowest seven branches of a tree was the best proxy for replant syndrome in our dataset, but geographic region had a stronger effect on growth patterns than soil health status. We found no significant correlation between chemical and physical soil variables and RS. Our findings based on DNA sequencing showed a higher eukaryotic (18S) Shannon alpha diversity in soil than in roots at all locations, while prokaryotic diversity (16S) was significantly higher in roots than in soil in only one region (Telemark). Comparing healthy and symptomatic soil, we found a significantly higher Shannon alpha diversity in healthy soil for 16S soil samples only in one region (Telemark), while there were no significant differences for 18S, and no significant differences in beta diversity for either. Again, region had a stronger effect on alpha biodiversity in 16S than soil health status, and was also significant in 18S. Average shoot length of the lowest seven branches was negatively correlated with 16S (soil) Shannon alpha diversity in RS soil only, a trend that was repeated but not significant for 18S in roots. We conclude that broad ecological perspectives are necessary to understand RS and highlight the need for studies focusing specifically on functional traits and the soil food web.

• Carlsen, Eira Catharine Lødrup; Pismeniuk, Anfisa; Wei, Jing; Ippach, Mats Rouven; Dörsch, Peter & Westermann, Sebastian [Show all 9 contributors for this article] (2026). FROM PEAT TO PONDS: LANDSCAPE HETEROGENEITY DRIVES METABOLIC NETWORKS AND GREENHOUSE GAS RELEASE FROM THAWING PERMAFROST. Full text in Research Archive Show summary

  As permafrost landscapes degrade, they transform into a hydrological mosaic of dry palsas, collapsing thermokarst slumps, and water-saturated ponds. This physical reorganization creates steep gradients in redox potential and organic matter quality, fundamentally altering the thermodynamic constraints on microbial metabolism. We investigated greenhouse gas (CO2, CH4, N2O) production potentials across several permafrost thaw gradients in sub-Arctic peatlands of Northern Norway, linking landscape-scale changes to genome-resolved metabolic networks. By integrating high-resolution metagenomics with organic matter and greenhouse gas production characterization, we found that thaw features act as distinct thermodynamic bioreactors. In water-saturated, anoxic peat layers, oxygen limitation selects for "slow" metabolic guilds specialized in fermentation and methanogenesis while other oxygenated features are constrained by the quality of organic matter—specifically the accumulation of polyphenols and aromatic compounds acts as a metabolic "latch". We show that the shift from oxic to anoxic conditions triggers a non-linear restructuring of the microbial network, where less efficient central metabolism drives high N2O and CH4 yields but suppressed CO2 production. These findings demonstrate that predicting the permafrost-carbon feedback requires mapping the "metabolic landscape"—where organic matter quality and redox thresholds ultimately tune the greenhouse gas release from thawing landscapes to the atmosphere.

• Riis-Pedersen, Christine; Carlsen, Eira Catharine Lødrup; Lejzerowicz, Franck Laurent Patrick; Hessen, Dag Olav & Eiler, Alexander (2026). HOW OPTICS AND THERMODYNAMICS SHAPE METHANE EMISSIONS FROM LAKES. Full text in Research Archive Show summary

  The interactions of light regime and physical stratification can be argued to dictate greenhouse gas flux through determining the thermodynamics in lake systems. Using geochemical profiling and metagenomics, we reconstructed metabolic networks in a wide range of lakes including ferruginous (iron-rich) and euxinic (sulfide-rich) systems. We observed significant methane accumulation in the anoxic monimolimnion—up to 420 µM in ferruginous lakes—yet surface levels remained low, indicating a highly efficient biofilter at the chemoclines. We identified a tight thermodynamic coupling between phototrophs and methanotrophs driven by oxidant regeneration. In ferruginous lakes, anoxygenic phototrophs likely use reduced iron (Fe2+) as an electron donor. This process regenerates oxidized iron (Fe3+), while in euxinic light energy is utilized to recycle essential electron acceptors such as SO42- (e.g., Chlorobium), required for anaerobic methane oxidation. Oxygenic phototrophs (e.g., Cyanobium) detected at and above the chemocline likely provide oxygen. This supply sustains aerobic methanotrophs like Crenothrix and Methylobacter even in suboxic waters. Hence methanotrophic capacity is ultimately constrained by optical properties selecting for low-intensity light anoxygenic or high-intensity oxygenic phototrophs. Consequently, levels of chromophoric dissolved organic matter determine methane oxidation rates. We conclude that chemoclines function as dynamic, light-powered engines for methane removal, sensitive to brownification and climate-induced shifts in stratification.

• Riis-Pedersen, Christine; Carlsen, Eira Catharine Lødrup; Hessen, Dag Olav; Lejzerowicz, Franck Laurent Patrick; Andersen, Tom & Dörsch, Peter [Show all 8 contributors for this article] (2025). Microbial drivers of methane cycling in meromictic as compared to holomictic lakes. Full text in Research Archive
• Carlsen, Eira Catharine Lødrup; Wei, Jing; Lejzerowicz, Franck Laurent Patrick; Ippach, Mats Rouven; Pismeniuk, Anfisa & Kjær, Sigrid Trier [Show all 10 contributors for this article] (2025). Greenhouse gas production kinetics and metabolic traits in thawing permafrost peat. Full text in Research Archive Show summary

  While numerous drivers of greenhouse gas emission (GGE) have been suggested to drive variabilities across thawing landscapes, experimental validations are still widely lacking . Here, I will present results from several experimental studies capturing drivers of GGE across thawing permafrost landscapes like redox, organic matter and microbial source community. Our findings reveal clear responses of the greenhouse gases to redox conditions across the landscape. CO2 production showed a drastic decline when O2 dropped below 100 μM; specifically, under anoxic conditions, CO2 yield and maximum net production rates decreased by around 90 % compared to oxic conditions. CH4 levels remained consistent across O2 gradients, until at least 6 months upon thawing. Functional groups like N2O reducers, fermenters, denitrifiers, and sulfur reducers increased under anoxic conditions, and the reduced CO2 production rates and yields under anoxic conditions were reflected by genomic changes towards reduced central metabolic efficiency. Our data thus points towards critical GGE thresholds under suboxic conditions across thawing landscapes. Moreoever, gas dynamics seem to be primarily influenced by permafrost conditions rather than source community colonization. Our experiments provide increased knowledge on the variable GGE across thawing permaforst landscapes influenced by variable redox conditions and permafrost´s organic matter legacy.

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